AP Biology Chemistry

Biology Is Multidisciplinary Emergent Properties = new properties that result from the interaction of components at a lower level of organization NOT –Properties NOT derived by adding original properties together Life is emergent properties Hierarchy of life

Elements and Compounds Chemistry = study of matter and interactions All living thing are made of matter Matter = has space and mass Mass = amount of matter Weight = measure of force of gravity on matter

Elements and Compounds Elements = matter that cannot be broken down into simple substances by ordinary means –92 natural; ? Artificial 96% of all life = CHON Other 4% = Ca, K, S, Na, Cl, Mg. Trace elements = minute quantities, essential to life (B, Cr, Cu, I, Fe, Mn, Sn, Zn)

Elements and Compounds Compounds = molecules composed of 2 or more elements chemically combined in a fixed ratio (NaCl) Compounds have different properties from their original elements

Atomic Structure/behavior 2 basic parts: nucleus and electron ‘cloud’ Nucleus = ‘center’; Protons (+1) and neutrons (0) All mass Electron ‘cloud’- electron(s) (-), negligible mass

Structure/behavior Atomic mass and number are written to the left of the symbol; mass on top Atomic number = number of protons (+) Atomic mass = no. protons (at. no.) + no. neutrons; mass number = average of all isotopes found in nature Isotope = same atom with different atomic mass due to differing numbers of neutrons –May be unstable - radioactive Atomic mass and number are written to the left of the symbol; mass on top Atomic number = number of protons (+) Atomic mass = no. protons (at. no.) + no. neutrons; mass number = average of all isotopes found in nature Isotope = same atom with different atomic mass due to differing numbers of neutrons –May be unstable - radioactive

Unstable Isotopes Radiation - spontaneous decay of subatomic particles or energy –Alpha (α), Beta (β), Gamma(γ) –Transformation into a stable element Radiation may be detected Radiation - spontaneous decay of subatomic particles or energy –Alpha (α), Beta (β), Gamma(γ) –Transformation into a stable element Radiation may be detected

Structure/behavior 3 uses for radiation; –Dating –Tracers –Cancer treatment 3 uses for radiation; –Dating –Tracers –Cancer treatment

Radioactive Dating N 2 absorbs energy from cosmic radiation –Converted into C 14 –C 14 spontaneously decays into C 12 Living organisms absorb N 2 and stop when they die; C 14 begins decaying Half-life = length of time it takes for half the substance to decay. Half-life is known; age can be calculated by knowing ratio of stable/radioactive isotope in fossils vs living organisms

Radiation Dating C 14 ’s half life = 5,700 Yr. Beta radiation rate = 15 rad/minute If the sample = 7.5 rads/min. = ½ gone or 5700 y.o. If the sample is ¼ gone, then the sample = 11,400 y.o. If 1/8 = ?

Radioactive Tracers Radioactive isotopes behave the same chemically –P, N 2, used to determine structure of DNA –I 2 in thyroid Radioactive isotopes behave the same chemically –P, N 2, used to determine structure of DNA –I 2 in thyroid

PET scan

Radiation: Cancer Treatment of cancer: Co Cause cancer; Chernobyl, Tokaimura; 3-Mile Island?

Structure/behavior Energy Levels: Electrons and orbitals Arrangement of outer electrons (valence) determines how atoms interact with other atoms (Chemistry) Electrons have potential energy because of their position (potential) relative to the nucleus Energy Levels: Electrons and orbitals Arrangement of outer electrons (valence) determines how atoms interact with other atoms (Chemistry) Electrons have potential energy because of their position (potential) relative to the nucleus

Energy = the ability to do work; move Potential = stored energy; due to position Energy = the ability to do work; move Potential = stored energy; due to position Kinetic = energy of motion

Energy Water on top of the hill = potential energy Energy flowing down the hill (gravity) has kinetic energy Water at the bottom of the hill has less potential energy

Structure/behavior Electron ‘shells’, ‘orbitals’ = distances that electrons are from the nucleus Electrons in the outer shells are more reactive and cause ‘chemical changes’ Outer shell = ‘valence shell’ Valence electrons = more reactive Electron ‘shells’, ‘orbitals’ = distances that electrons are from the nucleus Electrons in the outer shells are more reactive and cause ‘chemical changes’ Outer shell = ‘valence shell’ Valence electrons = more reactive

Energy potential energyElectrons in the atom have potential energy –Position relative to the nucleus –Electrons farther away from the nucleus have greater potential energy Electrons can absorb or lose energy

Bonds Attractions of atoms or molecules to form new compounds Three types: –Covalent –Ionic –Hydrogen

Structure/behavior Bonding = attractions formed between atoms caused by the interactions of valence electrons Number of bonds = no. of electrons gained/lost, shared to fulfill octet rule Bonding = attractions formed between atoms caused by the interactions of valence electrons Number of bonds = no. of electrons gained/lost, shared to fulfill octet rule

Structure/behavior Octet Rule = atoms are most stable when outer ‘shell’ has 8 electrons Four = do not gain or lose electrons (ions) but ‘share’ –Carbon, silicon Octet Rule = atoms are most stable when outer ‘shell’ has 8 electrons Four = do not gain or lose electrons (ions) but ‘share’ –Carbon, silicon

How Many Bonds Will Atoms Form? Carbon -Carbon - 4 NitrogenNitrogen - 3 OxygenOxygen - 2 Hydrogen - 1

What Are The Types of Bonds? Covalent Ionic Hydrogen

Covalent Bond Strongest type Electrons shared Diatomic molecules Carbon; –4 valence electrons –May be single, double, or triple –Si (?) Strongest type Electrons shared Diatomic molecules Carbon; –4 valence electrons –May be single, double, or triple –Si (?)

Covalent Bond Electrons may not be shared equally Polar - one atom may ‘share’ the electron(s) more; imbalanced bond –Polar Covalent Bond Nonpolar Covalent Bond = (?) Covalent bonds

Covalent Bond Polarity or non-polarity causes reactions between MOLECULES

Ionic Bonds Ionic Bond = formed between atoms that gain/lose valence electrons Not as strong as Covalent Usually only a few atoms or groups (polyatomic ions, CO 3, PO 4 ) Electrical charge; easily dissociated –One cause of pH Ionic Bond = formed between atoms that gain/lose valence electrons Not as strong as Covalent Usually only a few atoms or groups (polyatomic ions, CO 3, PO 4 ) Electrical charge; easily dissociated –One cause of pH Ionic bonds

Ionic Bonds Ions may dissociate easily (freely) in water Causes the water to become an electrolyte In living systems, the amount of (+) or (–) is measured as pH Nervous, muscular system

Hydrogen Bonds Attraction between (+) and (-) of adjacent molecule “Most” important in biology Weakest of the three Molecules have polar sites in their structure

and Function Bonds and Function Shape of the molecule created by bonding forces determines function Ex. Proteins have specific shapes that allow only another molecule with the right shape to fit; –Makes life chemistry possible Shape of the molecule created by bonding forces determines function Ex. Proteins have specific shapes that allow only another molecule with the right shape to fit; –Makes life chemistry possible

Structure/behavior Chemical equations are shorthand for reactions Reactants and Products Chemical formula vs. structural formula Equilibrium

Water

Water Life evolved in water (oceans) ¾ of earth covered with water 70-90% of organisms are water Properties of water make life possible Philic = loving Phobic = fearing Hydro = water

Exists in all 3 states on the planet

Properties of Water Adhesive Cohesive Surface tension High specific heat Expands as is freezes Universal solvent

Water: Hydrogen bonding

Water Properties Adhesive = adheres to other substances hydrophilic substances (glass, metals) Cohesive = adheres to itself Adhesion and cohesion create Capillarity in trees (transpiration) Adhesive = adheres to other substances hydrophilic substances (glass, metals) Cohesive = adheres to itself Adhesion and cohesion create Capillarity in trees (transpiration)

Water- Properties Surface tension - beading, ex. waterstriders

High Specific Heat Heat = total kinetic energy (motion) created by moving molecules. calorie = amount of heat needed to raise the T of 1 g of water 1 o C. Kilocalorie = 1000 cal.; Kcal or C Specific heat of water is very high –H bond absorb heat when broken and release heat when formed. Slow to change Temperature Heat = total kinetic energy (motion) created by moving molecules. calorie = amount of heat needed to raise the T of 1 g of water 1 o C. Kilocalorie = 1000 cal.; Kcal or C Specific heat of water is very high –H bond absorb heat when broken and release heat when formed. Slow to change Temperature

Water: Specific Heat Water will act as a heat ‘sink’, traps heat during summer… Slowly releases heat during winter Moderates earth’s climate; coastal areas milder

High Heat of Vaporization Heat of vaporization = amount of heat energy needed to cause a liquid to evaporate; (water = 540 cal/g) –H bonds must be broken before water molecules can absorb heat energy Heat of vaporization = amount of heat energy needed to cause a liquid to evaporate; (water = 540 cal/g) –H bonds must be broken before water molecules can absorb heat energy

High Heat of Vaporization Evaporative cooling = cooling of a surface as a liquid evaporates Molecules with the highest energy evaporate fastest, –Molecules with less heat energy are left behind (less heat = cooler) Radiators, dogs pant, Homeostasis Evaporative cooling = cooling of a surface as a liquid evaporates Molecules with the highest energy evaporate fastest, –Molecules with less heat energy are left behind (less heat = cooler) Radiators, dogs pant, Homeostasis

Expands as it Freezes Water contracts as it cools until 4 o C then it expands (9%); becomes less dense (floats). Bodies of water freeze at the top; insulation for life below Colder water from bottom re-circulates nutrients to the surface (life) Water contracts as it cools until 4 o C then it expands (9%); becomes less dense (floats). Bodies of water freeze at the top; insulation for life below Colder water from bottom re-circulates nutrients to the surface (life)

‘Universal’ Solvent Non-polar substances Due to Polarity; (+) end pulls (-) end Solution = mixture of two or more substances –Air –Solvent = dissolving agent (water); aqueous solution, alcohol – tincture –Solute = substance being dissolved Non-polar substances Due to Polarity; (+) end pulls (-) end Solution = mixture of two or more substances –Air –Solvent = dissolving agent (water); aqueous solution, alcohol – tincture –Solute = substance being dissolved

Measurement of Solutions Percentage Molarity – measure of the amount of solute dissolved in the solvent pH – measure of H ions in the solution

Molarity Mole = 1 molecular weight dissolved in 1 liter of solvent (water) –Ex. 1 mole of glucose = 180g dissolved in 1 liter of water. 1M glucose Molarity is convenient for combining substances and for describing concentration (1.0M, 0.5M, 0.1M) Mole = 1 molecular weight dissolved in 1 liter of solvent (water) –Ex. 1 mole of glucose = 180g dissolved in 1 liter of water. 1M glucose Molarity is convenient for combining substances and for describing concentration (1.0M, 0.5M, 0.1M)

pH Measure of amount of H + in solution Range of measure from = ‘acid’ 7-14 = ‘base’, ‘alkaline’ (alkalinity) Measure of amount of H + in solution Range of measure from = ‘acid’ 7-14 = ‘base’, ‘alkaline’ (alkalinity)

pH In water, (H 2 0) a hydrogen atom may dissociate from the oxygen to form: H 2 O + H 2 O H OH - H = (hydronium) OH - = hydroxide

pHpH In ‘pure’ water, the amount of H 3 O + = OH - : H 2 O + H 2 O H 3 O + + OH - Equilibrium ( not ionized) In ‘pure’ water, the amount of H 3 O + = OH - : H 2 O + H 2 O H 3 O + + OH - Equilibrium ( not ionized)

pH In equilibrium, number of H + in solution = 1/10,000, Equilibrium = pH 7 = ‘neutral’ ‘p’ = concentration pH = concentration of H +

pH In equilibrium: H+ = (1/10,000,000) OH - = (1/10,000,000) Total of H + + OH - = (14) If H+ = 1/1,000,000 = (6) OH- = 10 -8

pH A change in pH number (7 to 6) is exponential (tenfold) 1/10,000,000 (1 in 10 million) to: 1/1,000,000 (1 in 1 million) 7 to 5 = 100 fold increase in H+ 5.5 to 8.5 = 1000x increase (major change) –Pollution

pH Acids (‘acidic’) are substances that cause water to release H+ in solution (lower pH) Bases (alkaline) release OH- in solution pH always totals 14; if pH = 5 then concentration of OH = (?) If pH = 9, then concentration of OH (?)

pH Most biotic solutions = 6-8; –Stomach = Acid rain SO 2, NO 2 mix w/ water in atmosphere –Lowers pH of lakes, soil

pH Buffers = substance that prevents sudden, large changes in pH, weak acids or bases (bicarbonate)

Properties of Water Cohesive; H bond Adhesive; H bond High specific heat; H bond High heat of vaporization; H bond Expands as it freezes ‘Universal’ solvent; polarity